Table S1. Xoo strain MAI1 genes identified as differentially expressed in planta by microarray analysis.
GenBank_Accn / Library origin† / N. seq‡ / Putative function / Organism†† / e-value / Size / Timepoints∥ / Xanthomonas oryzae genome¶ /1d / 3d / 6d / MAFF 311018 / KACC10331 / PXO99A / BLS256 / BAI3 /
Protein synthesis
FI978291 / 1 / 1 / translation elongation factor Tu / Xoo PXO99A / 7.0E-16 / 836 / + / + / + / + / + / +
FI978292 / 1 / 1 / 30S ribosomal protein S8 / Xcc str. ATCC 33913 / 5.0E-41 / 821 / - / + / + / + / + / + / +
FI978280 / 2 / 12 / rRNA-23S ribosomal RNA / Xoo PXO99A / 0 / 557 / - / + / + / + / + / +
FI978284 / 1 and 2 / 22 / rRNA-23S ribosomal RNA / Xoo KACC10331 / 0 / 535 / + / + / + / + / + / +
Biological process unknown
FI978294 / 1 / 1 / No protein match (NPM) / - / - / 1203 / - / - / - / - / - / -
FI978293 / 1 / 1 / NPM / - / - / 974 / + / + / - / - / - / - / -
FI978295 / 1 / 1 / NPM / - / - / 1233 / + / - / - / - / - / -
FI978297 / 1 / 1 / NPM / - / - / 906 / + / - / - / - / - / -
FI978298 / 1 / 1 / NPM / - / - / 975 / + / - / - / - / - / -
FI978299 / 1 / 1 / NPM / - / - / 1499 / + / - / - / - / - / -
FI978300 / 1 / 1 / NPM / - / - / 1122 / - / - / - / - / - / -
FI978301 / 1 / 1 / NPM / - / - / 1659 / + / - / - / - / - / -
FI978302 / 1 / 1 / NPM / - / - / 674 / - / - / - / - / - / - / -
FI978303 / 1 / 1 / NPM / - / - / 1232 / + / - / - / - / - / -
FI978236 / 1 / 1 / NPM / - / - / 252 / - / - / + / + / +
FI978234 / 1 / 1 / NPM / - / - / 850 / - / - / - / + / +
FI978244 / 1 / 2 / NPM / - / - / 849 / - / - / - / - / + / +
FI978268 / 1 / 6 / NPM / - / - / 266 / - / + / + / + / + / +
FI978101 / 1 / 1 / NPM / - / - / 409 / + / - / - / - / - / -
FI978177 / 1 / 1 / NPM / - / - / 399 / + / - / - / - / - / -
FI978197 / 1 / 1 / NPM / - / - / 248 / - / - / - / - / - / -
FI978168 / 1 / 1 / NPM / - / - / 128 / - / - / - / + / - / -
FI978092 / 1 / 1 / NPM / - / - / 619 / - / - / - / - / - / +
M1PG05BGS2 / 1 / 1 / NPM / - / - / 85 / + / + / + / + / + / + / +
FI978077 / 1 / 1 / NPM / - / - / 135 / - / + / + / - / - / + / + / +
FI978163 / 1 / 1 / NPM / - / - / 145 / + / - / - / + / - / +
M1P4B2 / 1 / 1 / NPM / - / - / 112 / + / - / - / + / - / +
FI978179 / 1 / 1 / NPM / - / - / 369 / - / + / + / + / + / +
FI978172 / 1 / 1 / NPM / - / - / 203 / - / + / + / + / + / +
FI978158 / 1 / 1 / NPM / - / - / 345 / - / + / + / + / + / +
FI978311 / 1 / 1 / NPM / - / - / 903 / + / - / - / - / - / -
FI978281 / 1 / 12 / NPM / - / - / 464 / - / - / - / + / + / -
FI978314 / 1 / 1 / NPM / - / - / 720 / + / - / - / + / + / -
FI978310 / 1 / 1 / NPM / - / - / 942 / + / - / - / - / - / -
FI978308 / 1 / 1 / NPM / - / - / 931 / + / - / - / - / - / -
FI978317 / 1 / 1 / NPM / - / - / 1175 / + / - / - / - / - / -
FI978273 / 1 / 7 / NPM / - / - / 897 / + / - / - / - / - / -
FI978320 / 1 / 1 / NPM / - / - / 1471 / - / - / - / - / - / -
FI978321 / 1 / 1 / NPM / - / - / 1902 / - / - / - / - / - / -
FI978086 / 1 / 1 / NPM / - / - / 544 / - / - / - / - / - / - / -
FI978070 / 1 / 1 / NPM / - / - / 478 / - / - / - / - / - / +
FI978068 / 1 / 1 / NPM / - / - / 638 / - / + / + / - / - / - / - / -
FI978327 / 2 / 1 / NPM / - / - / 876 / - / - / - / - / - / - / -
FI978316 / 2 / 1 / NPM / - / - / 1157 / + / + / - / - / - / - / -
FI978296 / 2 / 2 / NPM / - / - / 1529 / + / - / - / - / - / -
FI978323 / 1 / 1 / NPM / - / - / 933 / - / - / - / - / - / -
FI978322 / 2 / 1 / NPM / - / - / 861 / + / - / - / - / - / -
Hypothetical protein
FI978312 / 1 / 1 / probable secretion protein / Xoc BLS256 / 9.0E-29 / 824 / + / - / - / - / + / +
FI978313 / 1 / 1 / hypothetical protein XOO1688 / Xoo KACC10331 / 1.0E-14 / 894 / + / + / + / + / + / - / -
FI978245 / 1 / 2 / hypothetical protein XOO4599 / Xoo KACC10331 / 4.0E-07 / 821 / - / + / + / + / - / +
FI978248 / 1 / 2 / hypothetical protein Xoryp_17850 / Xoc BLS256 / 2.0E-12 / 464 / + / + / + / + / + / +
FI978249 / 1 / 2 / probable secretion protein / Xoc BLS256 / 5.0E-55 / 408 / + / - / - / - / + / +
FI978256 / 1 / 3 / hypothetical protein XAC3725 / Xac str. 306 / 3.0E-35 / 846 / - / - / + / + / - / +
FI978269 / 1 / 6 / hypothetical protein XAC3314 / Xac str. 306 / 4.0E-54 / 795 / + / - / - / - / - / +
FI978272 / 1 / 5 / hypothetical protein Xoryp_04315 / Xoc BLS256 / 3.0E-64 / 409 / + / + / + / + / + / +
FI978278 / 1 / 9 / hypothetical protein XAC0817 / Xac str. 306 / 1.0E-39 / 782 / - / + / + / + / + / +
FI978283 / 1 / 17 / hypothetical protein XAC3968 / Xac str. 306 / 3.0E-05 / 471 / - / + / + / + / + / +
FI978285 / 1 / 26 / hypothetical protein XOO1934 / Xoo KACC10331 / 5.0E-13 / 774 / - / + / + / + / + / +
FI978315 / 1 / 1 / hypothetical protein / Xoo KACC10331 / 8.0E-39 / 867 / - / + / + / - / - / +
FI978160 / 1 / 1 / hypothetical protein / Xoo MAFF 311018 / 0 / 452 / - / + / + / + / + / +
FI978151 / 1 / 1 / hypothetical protein XOO1934 / Xoo KACC10331 / 0 / 366 / - / + / + / + / + / + / +
FI978079 / 1 / 1 / hypothetical protein XAC0016 / Xac str. 306 / 0 / 596 / + / + / + / + / + / + / +
FI978082 / 1 / 1 / hypothetical protein XAC0817 / Xac str. 306 / 0 / 287 / - / + / + / + / + / + / + / +
FI978175 / 1 / 1 / hypothetical protein XAC3525 / Xac str. 306 / 0 / 292 / + / - / - / + / + / +
FI978063 / 1 / 1 / hypothetical protein / Xoo PXO99A / 0 / 1144 / + / - / + / + / + / + / +
FI978067 / 1 / 1 / conserved hypothetical protein / Xoo MAFF 311018 / 0 / 537 / - / + / + / + / + / +
FI978198 / 1 / 1 / hypothetical protein / Xoo MAFF 311018 / 0 / 322 / + / + / + / + / + / +
FI978169 / 1 / 1 / hypothetical protein / Xoo PXO99A / 0 / 355 / - / - / - / + / + / +
FI978164 / 1 / 1 / conserved hypothetical protein / Xoo MAFF 311018 / 0 / 438 / + / + / + / + / + / +
FI978071 / 1 / 1 / hypothetical protein XOO_3844 / Xoo MAFF 311018 / 0 / 507 / - / + / + / + / + / +
FI978304 / 2 / 1 / hypothetical protein XOO1051 / Xoo KACC10331 / 1.0E-87 / 823 / - / + / + / + / + / -
FI978305 / 2 / 1 / hypothetical protein xccb100_3708 / Xcc str. ATCC 33913 / 4.0E-18 / 855 / + / - / - / - / - / +
FI978306 / 2 / 1 / conserved hypothetical protein / Xoo PXO99A / 2.0E-45 / 805 / - / - / - / + / - / -
FI978307 / 2 / 1 / hypothetical protein XCC2965 / Xcc str. ATCC 33913 / 3.0E-12 / 835 / - / - / - / - / - / -
FI978237 / 2 / 2 / hypothetical protein / Xoo PXO99A / 8.0E-36 / 843 / - / + / + / + / + / +
FI978251 / 2 / 3 / hypothetical protein XAC1497 / Xac str. 306 / 5.0E-07 / 610 / + / - / - / - / - / +
FI978239 / 1 and 2 / 2 / hypothetical protein XCC2966 / Xcc str. ATCC 33913 / 7.0E-11 / 244 / + / - / - / - / - / -
FI978240 / 1 and 2 / 2 / hypothetical protein XCC0647 / Xcc str. ATCC 33913 / 1.0E-62 / 791 / + / - / - / - / - / +
FI978252 / 1 and 2 / 2 / hypothetical protein XOO0776 / Xoo KACC10331 / 1.0E-57 / 785 / + / + / + / + / + / + / +
FI978265 / 1 and 2 / 4 / hypothetical protein XCC4108 / Xcc str. ATCC 33913 / 3.0E-83 / 500 / + / - / - / + / - / +
FI978289 / 1 and 2 / 34 / hypothetical protein CLOSS21_00494 / Xoo PXO99A / 2.0E-20 / 635 / + / + / + / + / + / +
FI978253 / 1 and 2 / 2 / hypothetical protein YintA_01003971 / Xoo MAFF 311018 / 3.0E-24 / 802 / + / + / + / + / +
Cell envelope & motility
FI978319 / 1 / 1 / type IV pilin / Xoc BLS256 / 3.0E-13 / 767 / + / + / + / + / + / +
FI978267 / 1 / 5 / fimbrial assembly protein / Xoo PXO99A / 1.0E-61 / 638 / + / + / + / + / + / +
FI978162 / 1 / 1 / outer membrane antigen / Xoo KACC10331 / 0 / 129 / - / + / + / + / + / +
FI978178 / 1 / 1 / pilin / Xoo KACC10331 / 0 / 377 / + / + / + / + / + / +
FI978318 / 2 / 1 / PilY1 protein / Xoo MAFF 311018 / 2.0E-31 / 816 / + / + / + / + / + / +
FI978286 / 1 and 2 / 23 / putative glycosyl transferase / Xoo KACC10331 / 1E-162 / 1017 / - / + / + / + / - / +
FI978238 / 1 and 2 / 2 / putative glycosyl transferase / Xoo KACC10331 / 1.0E-37 / 828 / - / + / + / + / - / +
Phage related & IS elements
FI978231 / 1 / 2 / ISXo1 transposase (IS5 family) / Xoo PXO99A / 7.0E-40 / 839 / + / + / - / - / + / + / +
FI978232 / 1 / 2 / ISXo1 transposase (IS5 family) / Xoo PXO99A / 5.0E-39 / 803 / + / - / - / + / + / +
FI978246 / 1 / 2 / transposase / Xoo PXO99A / 2.0E-08 / 937 / - / + / + / + / + / +
FI978241 / 1 / 2 / transposase (IS4 family) / Xoo KACC10331 / 8.0E-41 / 825 / - / + / + / + / + / + / +
FI978254 / 1 / 3 / IS1478 transposase (IS5 family) / Xoo KACC10331 / 9.0E-19 / 173 / + / - / + / + / + / + / +
FI978255 / 1 / 2 / ISXoo5 transposase (IS5 family) / Xoc BLS256 / 1.0E-21 / 813 / + / + / + / + / + / +
FI978258 / 1 / 3 / ISXoo15 transposase (IS30 family) / Xoo KACC10331 / 6.0E-39 / 746 / - / + / + / + / + / +
FI978261 / 1 / 4 / ISXoo5 transposase (IS5 family) / Xoc BLS256 / 6.0E-26 / 340 / + / + / + / + / + / +
FI978262 / 1 / 4 / ISXo8 transposase (IS5 family) / Xoo PXO99A / 6.0E-29 / 790 / + / + / + / + / + / +
FI978270 / 1 / 7 / putative transposase / Xoo KACC10331 / 1.0E-24 / 488 / + / + / + / + / + / +
FI978271 / 1 / 7 / gene transfer agent (GTA) like protein / Pl DS-1 / 8.0E-50 / 788 / + / - / - / - / - / -
FI978274 / 1 / 8 / ISXoo15 transposase (IS30 family) / Xoo MAFF 311018 / 4.0E-49 / 695 / + / + / + / + / + / +
FI978276 / 1 / 8 / IS1404 transposase (IS3 family) / Xoc BLS256 / 3.0E-27 / 728 / + / + / + / + / + / +
FI978287 / 1 / 26 / IS30 family transposase / Xoo KACC10331 / 2.0E-43 / 323 / + / + / + / + / + / +
FI978288 / 1 / 28 / putative transposase / Xoc BLS256 / 1E-164 / 1659 / + / + / + / + / + / + / +
FI978076 / 1 / 1 / putative transposase / Xoo KACC10331 / 0 / 688 / - / + / + / + / + / + / +
FI978147 / 1 / 1 / ISXoo15 transposase (IS30 family) / Xoo MAFF 311018 / 0 / 549 / + / + / + / + / + / + / +
FI978078 / 1 / 1 / transposase / Xoo MAFF 311018 / 0 / 413 / + / + / + / + / + / + / +
FI978084 / 1 / 1 / putative transposase / Xoo MAFF 311018 / 0 / 323 / + / + / + / + / + / + / +
FI978069 / 1 / 1 / ISXoo15 transposase (IS30 family) / Xoo KACC10331 / 0 / 708 / - / + / + / + / + / + / +
FI978174 / 1 / 1 / putative transposase / Xoo KACC10331 / 0 / 144 / - / + / + / + / + / + / +
FI978106 / 1 / 1 / putative transposase / Xoo PXO99A / 1.0E-59 / 281 / - / + / + / + / + / +
FI978083 / 1 / 1 / putative transposase / Xoo KACC10331 / 0 / 671 / - / + / + / + / + / +
FI978099 / 1 / 1 / putative transposase / Xoo KACC10331 / 3.0E-23 / 457 / + / + / + / + / + / + / +
FI978109 / 1 / 1 / IS1478 transposase (IS5 family) / Xoo KACC10331 / 0 / 178 / - / + / + / + / + / +
FI978233 / 2 / 1 / ISXo8 transposase (IS5 family) / Xoo PXO99A / 2.0E-21 / 887 / + / + / + / + / + / +
FI978250 / 2 / 3 / prophage Lp2 protein 6 / Xoo PXO99A / 6.0E-46 / 702 / - / + / + / + / + / +
Metabolism
FI978324 / 1 / 1 / haemolysin III / Xcc str. ATCC 33913 / 5.0E-17 / 853 / - / - / - / - / - / -
FI978325 / 1 / 1 / secreted xylanase / Xoc BLS256 / 9.0E-26 / 707 / + / + / + / + / + / -
FI978242 / 1 / 2 / glycine dehydrogenase / Xoo PXO99A / 6.0E-20 / 738 / + / + / + / + / + / +
FI978290 / 1 / 38 / dTDP-glucose 4,6-dehydratase / Xoo KACC10331 / 3.0E-69 / 496 / - / + / + / + / + / +
FI978181 / 1 / 1 / cellulase / Xoo KACC10331 / 0 / 262 / + / + / + / + / + / +
FI978088 / 1 / 1 / dTDP-glucose 4,6-dehydratase / Xoo KACC10331 / 0 / 503 / - / - / + / + / + / + / +
FI978167 / 1 / 1 / integrase, catalytic region / Nw / 0 / 287 / - / - / - / + / + / +
FI978235 / 2 / 2 / putative peptidase, S54 (rhomboid) / Xoo PXO99A / 5.0E-33 / 484 / - / - / - / + / + / +
FI978277 / 2 / 10 / ATPase / Xoo KACC10331 / 3.0E-45 / 346 / + / + / + / - / - / -
FI978279 / 1 and 2 / 9 / ribonucleoside-diphosphate reductase, beta subunit / Xoo PXO99A / 2.0E-29 / 530 / + / + / + / + / + / +
Signal Transduction
FI978266 / 1 / 5 / colicin I receptor / Xoc BLS256 / 6.0E-78 / 796 / - / + / + / + / + / +
Secretion, transport & binding proteins
FI978326 / 1 / 1 / probable colicin V secretion atp-binding protein / Xoc BLS256 / 3.0E-41 / 819 / - / - / - / - / + / +
FI978328 / 1 / 1 / probable TonB-dependent receptor / Xoc BLS256 / 2.0E-49 / 858 / + / + / + / + / + / + / +
FI978329 / 2 / 1 / TonB-dependent receptor / Xoc BLS256 / 8.0E-34 / 858 / + / + / + / + / + / +
FI978247 / 1 / 2 / magnesium and cobalt transport protein / Xoo KACC10331 / 2.0E-39 / 281 / - / + / + / + / + / +
FI978259 / 1 / 3 / ATP-binding protein of ABC transporter / Xoo MAFF 311018 / 1.0E-32 / 738 / + / + / + / + / - / +
FI978093 / 1 / 1 / probable secretion protein / Cv / 0 / 549 / - / - / - / - / - / +
FI978105 / 1 / 1 / probable secretion protein / Cv / 0 / 409 / - / - / - / - / - / +
FI978095 / 1 / 1 / ATP-binding protein of ABC transporter / Xoo MAFF 311018 / 0 / 520 / + / + / + / + / + / +
FI978102 / 1 / 1 / putative secreted protein / Xoo PXO99A / 0 / 293 / - / + / + / + / + / +
FI978243 / 1 / 2 / putative secreted protein / Xoc BLS256 / 6.0E-20 / 442 / - / + / + / + / + / +
FI978257 / 1 / 3 / putative secreted protein / Xcv str. 85-10 / 3.0E-32 / 231 / + / + / + / + / + / +
FI978275 / 1 and 2 / 9 / colicin V secretion/processing ATP-binding protein CvaB / Xoo PXO99A / 8.0E-91 / 637 / - / + / + / + / + / + / +
Virulence-related sequence
FI978263 / 1 / 3 / HrpF protein / Xoo KACC10331 / 3.0E-75 / 744 / + / + / + / + / + / + / +
FI978149 / 1 / 1 / Avr/Pth14 (avr/pth14) gene / Xoc BLS256 / 9.0E-58 / 887 / + / + / - / - / + / + / +
FI978260 / 1 / 3 / virulence regulator / Xoo PXO99A / 3.0E-47 / 769 / + / + / + / + / + / +
FI978282 / 1 and 2 / 17 / avirulence protein AvrBs3/pth family / Xoc BLS256 / 1.0E-19 / 397 / + / + / + / + / + / +
ACD57163 / PCR§ / 1 / XopX effector protein / Xoo PXO99A / 0 / 509 / + / + / + / + / + / + / + / +
AF275267 / PCR / 1 / avirulence protein gene (avrXa7) / Xoo KACC10331 / 0 / 725 / + / + / + / + / + / + / +
BAE68417 / PCR / 1 / leucin rich protein / Xoo MAFF 311018 / 0 / 390 / + / + / + / + / + / + / +
ACD60316 / PCR / 1 / Rhs element Vgr protein / Xoo PXO99A / 0 / 618 / + / + / + / + / + / + / +
† SSH library and/or libraries in which the clone was identified, where 1 corresponds to SSH library Xoo strain M1/PXO86, and 2 to SSH library Xoo strain M1/Xoc BLS256.